X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FNucleotideColourScheme.java;h=899fc60ae99d22f2cc372d99e22a543480dd3534;hb=d70d7e5bc8da1189f44709b6ec59ea1e23f6f557;hp=9768d9a34f7421e62af65a93795869275e7ea49b;hpb=174230b4233d9ce80f94527768d2cd2f76da11ab;p=jalview.git

diff --git a/src/jalview/schemes/NucleotideColourScheme.java b/src/jalview/schemes/NucleotideColourScheme.java
index 9768d9a..899fc60 100755
--- a/src/jalview/schemes/NucleotideColourScheme.java
+++ b/src/jalview/schemes/NucleotideColourScheme.java
@@ -44,10 +44,10 @@ public class NucleotideColourScheme extends ResidueColourScheme
      *
      * @return DOCUMENT ME!
      */
-    public Color findColour(String n)
+    public Color findColour(char c)
     {
         // System.out.println("called"); log.debug
-        return colors[((Integer) (ResidueProperties.nucleotideHash.get(n))).intValue()];
+        return colors[ResidueProperties.nucleotideIndex[c]];
     }
 
     /**
@@ -58,13 +58,14 @@ public class NucleotideColourScheme extends ResidueColourScheme
      *
      * @return DOCUMENT ME!
      */
-    public Color findColour(String n, int j)
+    public Color findColour(char c, int j)
     {
-        if ((threshold == 0) || aboveThreshold(n, j))
+        Color currentColour;
+        if ((threshold == 0) || aboveThreshold(c, j))
         {
             try
             {
-                currentColour = colors[((Integer) (ResidueProperties.nucleotideHash.get(n))).intValue()];
+                currentColour = colors[ ResidueProperties.nucleotideIndex[c]];
             }
             catch (Exception ex)
             {
@@ -77,7 +78,7 @@ public class NucleotideColourScheme extends ResidueColourScheme
         }
 
         if(conservationColouring)
-         applyConservation(j);
+         currentColour = applyConservation(currentColour, j);
 
        return currentColour;
     }